After reading the rules several times, and not coming up with the answer tot his question, I am assuming the heroes continue to lose CTs whenever the OL shuffles his deck. I would truly appreciate it if someone could confirm or deny it.

Confirmed. When in a dungeon, if the overlord shuffles their deck, they get the standard number of 3 conquest tokens.

Keep in mind though, that if the Overlord shuffles their deck twice while on the same level of dungeon the heroes are forced to flee.

Also note, that when the Overlord gains CT (XP) in Road to Legends, the Heroes DON'T lose CT (XP)! It's a big main difference between the RtL "reward" system and the one in Journey Through The Dark.

Elric of Melniboné said:

+1.

Any effect from vanilla that causes the heroes to lose CT, in the advanced campaign will cause the OL to gain CT instead.